Aim: To estimate the prevalence of diabetes, heart disease, hypertension and stroke in self-report and hospital data in two cohorts of women; measure sensitivity and agreement between data sources; and compare between cohorts.Methods: Women born between 1946–1951 and 1921–1926 who participated in the Australian Longitudinal Study on Women's Health (ALSWH); were New South Wales residents; and admitted to hospital (2004–2008) were included in the present study. The prevalence of diabetes, heart disease, hypertension and stroke was estimated using self-report (case?1 at latest survey, case?2 across multiple surveys) and hospital records. Agreement (kappa) and sensitivity (%) were calculated. Logistic regression measured the association between patient characteristics and agreement.Results: Hypertension had the highest prevalence and estimates were higher for older women: 32.5% case?1, 45.4% case?2, 12.8% in hospital data (1946–1951 cohort); 57.8% case?1, 73.2% case?2, 38.2% in hospital data (1921–1926 cohort). Agreement was substantial for diabetes: ??=?0.75 case?1, ??=?0.70 case?2 (1946–1951 cohort); ??=?0.77 case?1, ??=?0.80 case?2 (1921–1926 cohort), and lower for other conditions. The 1946–1951 cohort had 2.08 times the odds of agreement for hypertension (95% CI 1.56 to 2.78; P?0.0001), and 6.25 times the odds of agreement for heart disease (95% CI 4.35 to 10.0; P?0.0001), compared with the 1921–1926 cohort.Conclusion: Substantial agreement was found for diabetes, indicating accuracy of ascertainment using self-report or hospital data. Self-report data appears to be less accurate for heart disease and stroke. Hypertension was underestimated in hospital data. These findings have implications for epidemiological studies relying on self-report or administrative data.